webread error(ncbi)

2 次查看（过去 30 天）
arash manbu
arash manbu 2020-12-2
回答： Rahul 2025-6-25
im trying to get some information from ncbi website using this code:
HepatitisC = getgenbank('NC_004102');
HepatitisC = HepatitisC.Sequence;
Hepatitisc_length = length(HepatitisC);
first_300_bases = seqdisp(HepatitisC(1:300));
figure
ntdensity(HepatitisC)
bases = basecount(HepatitisC);
figure
basecount(HepatitisC,'chart','pie');
title('Distribution of Nucleotide Bases for Hepatitis C Virus');
figure
dimers = dimercount(HepatitisC,'chart','bar');
title('Hepatitis C Dimer Histogram');
seqshoworfs(HepatitisC);
orfs = seqshoworfs(HepatitisC,'AlternativeStartCodons',true);
AND I RECIVE THIS ERROR:
Error using webread (line 122)
The connection to URL
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=NC_004102%5BAccession%5D' timed out after 5
seconds. Set options.Timeout to a higher value.
Error in getncbidata>accession2gi (line 315)
searchXML = webread(searchurl);
Error in getncbidata (line 181)
[giID,db] = accession2gi(accessnum,db,'quick');
Error in getgenbank (line 76)
[varargout{1:nargout}] = getncbidata(accessnum,'fileformat','GenBank','database','nucleotide',varargin{:});
Error in Hepatitis (line 1)
HepatitisC = getgenbank('NC_004102');
im new to matlab and i dont know how to solve this.
thanks

请先登录，再回答此问题。

回答（1 个）

Rahul
Rahul 2025-6-25
Hi @arash manbu,
I understand that you face the mentioned error of 'webread' while trying to obtain the data using 'getgenbank'. You can consider the following options to read the data correctlty:
  • Set a higher timout using the 'weboptions' function.
  • Obtain the data in a txt file using the 'websave' function with the weboptions defined.
  • Now read the data from the txt file using 'getbankread' function.
Here is an example:
wo = weboptions("Timeout", 10);
websave("output.txt", "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=950361812&rettype=gb&retmode=text&seq_start=6022&seq_stop=17213", wo);
data = genbankread("output.txt");
In recent MATLAB versions this issue has been resolved and just accessing data using 'getgenbank('NC_004102')' does not give the error.
The following MathWorks documentations can be referred:
'getgenbank': https://www.mathworks.com/help/bioinfo/ref/getgenbank.html
Thanks.

类别

在 Help Center 和 File Exchange 中查找有关 Sparse Matrices 的更多信息

标签

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by